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Sodium in PDB 1s5e: Cholera Holotoxin, Crystal Form 1

Enzymatic activity of Cholera Holotoxin, Crystal Form 1

All present enzymatic activity of Cholera Holotoxin, Crystal Form 1:
2.4.2.36;

Protein crystallography data

The structure of Cholera Holotoxin, Crystal Form 1, PDB code: 1s5e was solved by C.J.O'neal, E.I.Amaya, M.G.Jobling, R.K.Holmes, W.G.Hol, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.82 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 59.931, 108.230, 122.976, 90.00, 95.89, 90.00
R / Rfree (%) 16.7 / 20.5

Sodium Binding Sites:

The binding sites of Sodium atom in the Cholera Holotoxin, Crystal Form 1 (pdb code 1s5e). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Cholera Holotoxin, Crystal Form 1, PDB code: 1s5e:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 1s5e

Go back to Sodium Binding Sites List in 1s5e
Sodium binding site 1 out of 2 in the Cholera Holotoxin, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cholera Holotoxin, Crystal Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na241

b:23.7
occ:1.00
O A:TYR150 2.3 20.3 1.0
O A:LEU153 2.3 21.4 1.0
O A:HOH262 2.4 20.8 1.0
OG1 A:THR90 2.5 19.7 1.0
O A:ASN1 2.5 10.4 1.0
O A:THR90 2.5 23.9 1.0
C A:LEU153 3.3 22.2 1.0
C A:THR90 3.4 21.9 1.0
C A:TYR150 3.5 21.3 1.0
N A:THR90 3.6 21.6 1.0
CB A:THR90 3.6 21.8 1.0
CA A:THR90 3.7 22.2 1.0
C A:ASN1 3.7 12.5 1.0
N A:LEU153 4.1 22.8 1.0
CA A:SER151 4.1 23.6 1.0
CA A:LEU153 4.1 21.9 1.0
N A:ASN1 4.2 11.4 1.0
N A:SER151 4.2 22.3 1.0
N A:ASP154 4.2 22.9 1.0
CB A:LEU153 4.3 22.8 1.0
CA A:ASP154 4.4 24.2 1.0
CA A:TYR150 4.5 20.6 1.0
C A:SER151 4.5 24.3 1.0
O A:ASP3 4.5 10.7 1.0
O A:HOH252 4.5 30.9 1.0
N A:ALA91 4.5 22.7 1.0
C A:ALA89 4.6 21.8 1.0
CA A:ASN1 4.6 13.0 1.0
N A:ASP2 4.7 13.0 1.0
CA A:ASP2 4.7 14.3 1.0
CB A:TYR150 4.7 19.9 1.0
CB A:ALA89 4.7 22.3 1.0
CG2 A:THR90 4.8 23.1 1.0
O A:SER151 4.8 24.2 1.0
OD1 A:ASN1 4.8 15.3 1.0
N A:ASP3 4.8 13.5 1.0
N A:ASN152 4.9 25.1 1.0
OD1 A:ASP154 4.9 28.5 1.0
C A:ASP2 5.0 14.6 1.0
CA A:ALA89 5.0 21.4 1.0

Sodium binding site 2 out of 2 in 1s5e

Go back to Sodium Binding Sites List in 1s5e
Sodium binding site 2 out of 2 in the Cholera Holotoxin, Crystal Form 1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cholera Holotoxin, Crystal Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na241

b:23.3
occ:1.00
O B:HOH267 2.2 22.2 1.0
O B:LEU153 2.4 8.5 1.0
O B:TYR150 2.4 6.0 1.0
OG1 B:THR90 2.5 8.9 1.0
O B:THR90 2.5 8.8 1.0
O B:ASN1 2.5 7.7 1.0
C B:THR90 3.4 8.1 1.0
C B:LEU153 3.4 9.3 1.0
C B:TYR150 3.5 7.0 1.0
N B:THR90 3.5 6.8 1.0
CB B:THR90 3.6 8.7 1.0
CA B:THR90 3.7 7.9 1.0
C B:ASN1 3.8 10.8 1.0
N B:LEU153 4.1 8.7 1.0
CA B:SER151 4.2 7.2 1.0
CA B:LEU153 4.2 8.9 1.0
O B:HOH262 4.3 30.1 1.0
N B:SER151 4.3 6.4 1.0
N B:ASN1 4.3 9.0 1.0
N B:ASP154 4.3 9.6 1.0
O B:ASP3 4.3 9.4 1.0
O B:HOH257 4.4 28.1 1.0
CB B:LEU153 4.4 8.2 1.0
CA B:ASP154 4.5 10.6 1.0
CA B:TYR150 4.5 8.2 1.0
C B:SER151 4.5 9.7 1.0
C B:ALA89 4.5 7.6 1.0
CB B:ALA89 4.5 8.6 1.0
N B:ALA91 4.6 8.6 1.0
CA B:ASP2 4.7 12.1 1.0
N B:ASP2 4.7 10.8 1.0
CA B:ASN1 4.7 10.3 1.0
CG2 B:THR90 4.7 8.6 1.0
CB B:TYR150 4.7 8.2 1.0
N B:ASP3 4.8 10.5 1.0
O B:SER151 4.8 8.5 1.0
OD1 B:ASN1 4.8 14.3 1.0
OD1 B:ASP154 4.9 14.6 1.0
CA B:ALA89 4.9 7.6 1.0
C B:ASP2 4.9 11.7 1.0

Reference:

C.J.O'neal, E.I.Amaya, M.G.Jobling, R.K.Holmes, W.G.Hol. Crystal Structures of An Intrinsically Active Cholera Toxin Mutant Yield Insight Into the Toxin Activation Mechanism Biochemistry V. 43 3772 2004.
ISSN: ISSN 0006-2960
PubMed: 15049684
DOI: 10.1021/BI0360152
Page generated: Sun Oct 6 22:21:54 2024

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